Biophys Rev
DOI 10.1007/s12551-016-0247-1
REVIEW
Software for molecular docking: a review
Nataraj S. Pagadala 1 & Khajamohiddin Syed 2 & Jack Tuszynski 3,4
Received: 13 November 2016 / Accepted: 27 December 2016
# International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag Berlin Heidelberg 2017
Abstract Molecular docking methodology explores the be-
havior of small molecules in the binding site of a target pro-
tein. As more protein structures are determined experimentally
using X-ray crystallography or nuclear magnetic resonance
(NMR) spectroscopy, molecular docking is increasingly used
as a tool in drug discovery. Docking against homology-
modeled targets also becomes possible for proteins whose
structures are not known. With the docking strategies, the
druggability of the compounds and their specificity against a
particular target can be calculated for further lead optimization
processes. Molecular docking programs perform a search al-
gorithm in which the conformation of the ligand is evaluated
recursively until the convergence to the minimum energy is
reached. Finally, an affinity scoring function, ΔG [U total in
kcal/mol], is employed to rank the candidate poses as the sum
of the electrostatic and van der Waals energies. The driving
forces for these specific interactions in biological systems aim
toward complementarities between the shape and electrostat-
ics of the binding site surfaces and the ligand or substrate.
* Nataraj S. Pagadala
nattu251@gmail.com
1
Department of Medical Microbiology and Immunology, Li Ka Shing
Institute of Virology, 6-020 Katz Group Centre, University of
Alberta, Edmonton, Alberta T6G 2E1, Canada
2
Unit for Drug Discovery Research, Department of Health Sciences,
Faculty of Health and Environmental Sciences, Central University of
Technology, Bloemfontein 9300, Free State, South Africa
3
Department of Experimental Oncology, Cross Cancer Institute,
Edmonton, Alberta, Canada
4
Department of Physics, University of Alberta, Edmonton, Alberta,
Canada
Keywords Rigid body docking . Flexible docking . Docking
accuracy
Introduction
In modern drug discovery, protein–ligand or protein–protein
docking plays an important role in predicting the orientation
of the ligand when it is bound to a protein receptor or enzyme
using shape and electrostatic interactions to quantify it. The
van der Waals interactions also play an important role, in
addition to Coulombic interactions and the formation of hy-
drogen bonds. The sum of all these interactions is approximat-
ed by a docking score, which represents potentiality of bind-
ing. In the simplest rigid-body systems, the ligand is searched
in a six-dimensional rotational or translational space to fit in
the binding site, which can serve as a lead compound for drug
design (Alberg and Schreiber 1993).
The docking accuracy in a rigid-body approach is much
greater for bound complexes than uncomplexed molecules
(Shoichet and Kuntz 1991). Even though the observed
structural changes between the bound and free forms are
small, the difference in accuracy implies that the assump-
tion of rigidity is not fully warranted (Totrov and Abagyan
1994). Also, the difference between the near native struc-
tures and others far from native cannot be distinguished,
even with simple scoring functions such as measures of
surface complementarity (Katchalski-Katzir et al. 1992), solvent
accessible surface area (SASA) burial, solvation free energy,
electrostatic interaction energy, or the total molecular mechanics
energy (Shoichet and Kuntz 1991). Hence, the docking proce-
dures were improved by several groups by allowing for receptor
and ligand flexibility.
The entropy loss of a flexible ligand in rigid six body de-
grees of freedom in an anisotropic environment of the receptor

and the change in its internal energy upon binding can greatly
affect the binding affinity. Introducing local minimization of a
molecular-mechanics energy function such as in the
CHARMM package yields only limited improvement
(Brooks et al. 2009). Consequently, information regarding
the binding site location before the docking processes became
very important to increase the docking efficiency. There are
several cavity detection programs or online servers that can
detect putative active sites within proteins, e.g., GRID
(Goodford 1985), POCKET (Levitt and Banaszak 1992),
SURFNET (Laskowski 1995), PASS (Putative Active Sites
with Spheres) (Brady and Stouten 2000), and MMC (mapping
macromolecular topography) (Mezei 2003).
The earliest reported docking methods were based on the
lock-and-key assumption proposed by Fischer, stating that
both the ligand and the receptor can be treated as rigid bodies
and their affinity is directly proportional to a geometric fit
between their shapes (Mezei 2003). Later, the Binduced-fit^
theory proposed by Koshland suggested that the ligand and
receptor should be treated as flexible during docking
(Hammes 2002; Koshland 1963). Each backbone movement
affects multiple side chains in contrast to relatively indepen-
dent side chains. Thus, the sampling procedure in a fully flex-
ible receptor/ligand docking is of a higher order of magnitude
in terms of the number of degrees of freedom than in flexible
docking with a rigid receptor. Consequently, these flexible
docking algorithms not only predict the binding mode of a
molecule more accurately than rigid body algorithms, but also
its binding affinity relative to other compounds (Verkhivker
et al. 2000).
Over the last two decades, more than 60 different docking
tools and programs have been developed for both academic
and commercial, use such as DOCK (Venkatachalam et al.
2003) AutoDock (Österberg et al. 2002), FlexX (Rarey et al.
1996), Surflex (Jain 2003), GOLD (Jones et al. 1997), ICM
(Schapira et al. 2003), Glide (Friesner et al. 2004), Cdocker,
LigandFit (Venkatachalam et al. 2003), MCDock, FRED
(McGann et al. 2003), MOE-Dock (Corbeil et al. 2012),
LeDock (Zhao and Caflisch 2013), AutoDock Vina (Trott
and Olson 2010), rDock (Ruiz-Carmona et al. 2014), UCSF
Dock (Allen et al. 2015), and many others.
Although strategies in the ligand placement differ one
from another, these programs are broadly categorized as
ranging from incremental construction approaches, such
as FlexX (Rarey et al. 1996) to shape-based algorithms
(i.e., DOCK) (Kuntz et al. 1982), genetic algorithms
(GOLD) (Jones et al. 1997), systematic search techniques
(Glide, Schrödinger, Portland, OR 97201), and Monte
Carlo simulations (LigandFit) (Venkatachalam et al. 2003).
With the exception of GOLD, almost all current flexible
ligand docking programs treat the receptor as rigid (Jones
et al. 1997). These programs were evaluated to test their
abilities in producing the correct binding mode of a ligand
Biophys Rev
to its biological target and identifying the known com-
pounds with top scores in virtual screening trials. In order
to assesses the docking accuracy and mode of binding,
initially, FlexX was evaluated on a set of 19 protein–ligand
complexes, with a subsequent evaluation on a larger set of
200 complexes (Rarey et al. 1996). The docking accuracy of
Glide was assessed by redocking ligands from 282 co-
crystallized PDB complexes, while GOLD was validated on
100 and 305 complexes (Friesner et al. 2004; Jones et al.
1997). Further, ligandFit was reported for 19 protein–ligand
complexes (Venkatachalam et al. 2003), while DOCK has been
verified on several targets over the years (Bodian et al. 1993;
Debnath et al. 1999; Shoichet et al. 1993). Both AutoDock and
AutoDock Vina were calibrated using the same test set of 30
structurally known protein–ligand complexes with experimen-
tally determined binding constants (Österberg et al. 2002; Trott
and Olson 2010).
Among these programs, AutoDock Vina, GOLD, and
MOE-Dock predicted top ranking poses with best scores.
GOLD and LeDock were able to identify the correct ligand
binding poses. Both Glide (XP) and GOLD predict the poses
consistently with a 90.0% accuracy (Wang et al. 2016). It was
also shown that GOLD produced higher enrichment factors
than Glide in a virtual screening trial against Factor Xa,
whereas Glide outperformed GOLD against the same target
in a similar virtual screening trial. Overall, it was reported
recently that these docking programs are able to predict
experimental poses with root-mean-squared deviations
(RMSDs) averaging from 1.5 to 2 Å (Bissantz et al. 2000;
Dixon 1997). However, flexible receptor docking, especially
backbone flexibility in receptors, still presents a major chal-
lenge for the available docking methods.
Rigid body docking
Rigid body docking produces a large number of docked con-
formations with favorable surface complementarity, followed
by the reranking of the conformations using the free energy of
approximation. The fast Fourier transform (FFT) correlation
approach (Katchalski-Katzir et al. 1992) systematically ex-
plores the space of docked conformations using electrostatic
interactions (Mandell et al. 2001) or both electrostatic and
solvation terms (Chen et al. 2003), but the potential is
restricted to a correlation function form. Later, polar
Fourier correlations were used to accelerate the search for
candidate low-energy conformations (Ritchie and Kemp
2000). Additionally, other approaches such as computer
vision concepts (Wolfson and Nussinov 2000), Boolean
operations (Palma et al. 2000), and the genetic algorithms
(Gardiner et al. 2001) were also used. In fact, the Fourier
transform algorithm can also use spherical harmonic decom-
position to accelerate the search over 3D rotational space, as
Biophys Rev
used in FRODOCK. To further improve the FFT docking,
atomic contact energy is added to estimate the desolvation
energy in RDOCK and electrostatic correction in ZDOCK
(Bissantz et al. 2000; Metropolis and Ulam 1949).
There are also other types of useful FFT based rigid-body
docking tools without a 3D grid-based searching system, such
as Hex (Ritchie and Kemp 2000; Ritchie and Venkatraman
2010). HEX uses spherical polar Fourier correlations for both
rotational and translational space. Furthermore, the efficiency
of Fourier transform-based algorithms is further accelerated
computationally with the help of advanced software packages,
such as the 3D convolution library (Pierce et al. 2011), and
new hardware technologies, such as the graphics processing
unit (GPU) (Ritchie and Venkatraman 2010) and Cell BE
processor (Pons et al. 2012). The docking program ‘DOT’
performs a systematic rigid-body search of one molecule, car-
rying out both translational and rotational orientation on a
second molecule. Finally, the sum of intermolecular energies
of electrostatic and atomic desolvation energies as a correla-
tion function for all the generated configurations are computed
efficiently with FFTs (Roberts et al. 2013).
MEGADOCK is similar to ZDOCK in that it generates
docking conformations in a grid-based 3D space using an
FFT. But MEGADOCK calculations are 8.8 times faster than
ZDOCK due to a much simpler score function in which only
shape complementarity and electrostatics are considered
(Ohue et al. 2014a). Using these two programs, the core signal
process in the bacterial chemotaxis pathway has been identi-
fied (Matsuzaki et al. 2014). Later, a soft docking approach in
FFT was developed where the ligand and the receptor are
considered as rigid bodies, and their conformational changes
are calculated by allowing a certain degree of inter-protein
penetration (Katchalski-Katzir et al. 1992). These domain–
domain poses were also scored by binding energy and a
pseudo-energy term based on restraints derived from linker
and end-to-end distances in pyDockTET (tethered-docking).
The other programs include SOFTDOCK (Jiang and Kim
1991), BiGGER (Palma et al. 2000), and SKE-DOCK
(Terashi et al. 2007). For the sake of matching efficiency, each
grid point is given a value of ‘1’ when occupied by the protein
or ‘0’ otherwise. This grid-based system is similar to FFT-
based grid searches, except that it has simpler values on the
grid. Although the affinity of a ligand–protein complex is
determined mainly by complementary physical-chemistry fea-
tures, shape complementarity became an essential part in rigid
body docking programs (O’Sullivan et al. 1991). Apart from
electrostatics, the hydrophobic complementarity based on ge-
ometry was incorporated in the MolFit FFT program to cal-
culate the interface of a protein–protein complex (Katchalski-
Katzir et al. 1992). Recently, PIPER was developed to predict
mutual orientation of the two proteins using pairwise interac-
tion potential between the atoms i and j. The contributions to
the scoring function are evaluated in discretized 6D space as
the sum of terms representing shape complementarity, electro-
static, and desolvation energies. The structures obtained in
PIPER are very close to their native conformations due to
the decomposition of eigenvalue–eigenvector, which is the
key to the efficient use of this potential (Kozakov et al. 2006).
However, these algorithms are not well suited for unbound
crystal structures and yield many false-positives far from the
native complex, though they have good surface complemen-
tarity. To improve in silico prediction further, F2Dock was
developed, which also uses shape complementarity and scores
based on Coulombic potentials. This program is also struc-
tured to incorporate the Lennard-Jones potential and docking
solutions were reranked based on desolvation energy. These
contributions were shown to be effective in more than 70% of
the cases in a bound–unbound complex. The lowest RMSD
was improved by at least 0.5 Å for 45 bound–unbound com-
plexes and less than 1 Å was seen for 27 bound–bound com-
plexes (Bajaj et al. 2011). In fact, DOCK was one of the first
programs that involved shape complementarity through a set
of spheres in the determination of ligand–protein interactions.
The volume occupied by the ligand depends on the diameter
of the spheres inside the binding pocket of the protein (Kuntz
et al. 1982). The initial orientation of the ligand inside the
binding pocket is determined by a maximum clique detection
method based on distance compatibility. However, the data
can be accessed rapidly though geometric hashing by
matching features in triplets. The features are represented
in the form of spheres and are clustered as poses (Fischer
et al. 1993). SDOCK performs global searches by incor-
porating the van der Waals attractive potential, geometric
collision, screened electrostatic potential, and Lazaridis–
Karplus desolvation energy into the scoring function.
Structure flexibility was based on stepwise potentials that
were generated from the corresponding continuous forms
(Zhang and Lai 2011).
Cell-Dock also performs the global scan using the transla-
tional and rotational space of two molecules based on surface
complementarity and electrostatics. A paramount difference
with FTDock is that the value of the grid size is fixed in a
number of cells that reflects grid cell resolution and total span
in Angstroms (Pons et al. 2012). Furthermore, to reduce the
size of molecules from large compound libraries, shape com-
plementarity was introduced between ligand and protein in
MS-DOCK to perform efficient multiple conformation rigid-
body docking (Sauton et al. 2008). The contact surface be-
tween the ligand and the protein is further optimized by a
Gaussian shape fitting function in FLOG (Miller et al.
1994), CLIX (Lawrence and Davis 1992), FRED (McGann
et al. 2003), and PAS-Dock (Protein Alpha Shape-Dock)
(Tøndel et al. 2006) to perform rigid body docking.
The TagDock toolkit produces macromolecular com-
plexes from rigid monomers by generating randomly posed
docked pairs (decoys) that agree with inter-monomer distance

restraints determined experimentally by using a penalty for
each decoy (Smith et al. 2013). Examples of other docking
programs that use local shape featuring algorithms include
LZerD (Venkatraman et al. 2009), PatchDock (Schneidman-
Duhovny et al. 2005) and GAPDOCK (Gardiner et al. 2001).
Geometric hashing algorithms also perform a global protein–
protein docking using local shape descriptors, such as surface
patches in PatchDock (Harrison et al. 2002) or 3D Zernike
descriptors in LZerD (Venkatraman et al. 2009), between pro-
teins. Recently, an integrated algorithm, MEMDOCK
(Membrane Dock) was designed for docking within the mem-
branes. The method models both side chain and backbone
flexibility and performs rigid body optimization of the ligand
orientation using modified Patchdock and Fiberdock (Hurwitz
et al. 2016).
Accuracy of rigid body docking
Docking was considered successful if the binding of a ligand
into its active site was closer than a given threshold from the
X-ray solution. The DOCK program applied to aspartic pro-
tease of HIV resulted in a candidate inhibitor with high poten-
cy turned out to be several orders of magnitude too low for
clinical use. However, this molecule can be used as a lead
compound for the design of more potent inhibitors.
Ring and coworkers designed inhibitors against proteases
of schistosome and malaria parasites that are crucial to the
pathogenicity by using shape-complementarity function and
a simplified molecular-mechanics potential approximating the
interaction energy between the protease and ligand (Ring et al.
1993). The DOT program successfully predicted the electron
transfer complex of the positively charged cytochrome c to the
negative region on the cytochrome c oxidase surface formed
by subunit II (Roberts and Pique 1999). Out of 25 protein–
protein complexes tested using the BiGGER program, 22
complexes were near to native docked geometries with
C(alpha) RMS deviations ≤4.0 A from the experimental struc-
tures, of which 14 were found within the 20 top ranking solu-
tions (Palma et al. 2000). With the omission of water mole-
cules, the top-ranking solutions of the MolFit program using
geometric and geometric-electrostatic docking identify clus-
ters of nearly correct solutions with limited rotational freedom
at the interface for disassembled and unbound structures
(Heifetz et al. 2002). In round 1 of CAPRI (Critical
Assessment of PRediction of Interactions) experiments,
GAPDOCK correctly predicted 17 of 52 interprotein contacts
with target 1 and 27 of 52 contacts with target 2 compared to
those obtained by other methods (Gardiner et al. 2003). Using
PatchDock, out of 35 examples, 31 examples were shown to
have the lowest RMSD below 2 Å. In 26 cases, the correct
poses were ranked first, whereas in the other nine cases, the
correct solution is ranked among the first 30 conformations.
Biophys Rev
However, SymmDock only predicts structures with cyclic
symmetry. If the input monomers are with different symmetry
in its native complex, then SymmDock is not suitable for such
a prediction (Schneidman-Duhovny et al. 2005).
With simple unbound–bound target cases, 47% of the in-
terface contacts were correctly predicted by ZDOCK, demon-
strating its strength in binding site prediction (Wiehe et al.
2005). INTELEF, an updated version of SOFTDOCK, pre-
dicted 66 corrected solutions out of 83 with ranks in the top
2000 solutions (Li et al. 2007). Using the SE-Dock server, the
smallest RMSD between the model and experimental struc-
tures obtained were 3.307 and 3.324 Å, respectively. In the
docking step, out of eight targets, the SKE-DOCK server gen-
erated acceptable models with ligand RMSD of 10 Å or lower
for five targets. For the results of three targets, SKE-DOCK
failed in the geometric docking because of improper confor-
mations obtained during the docking step (Terashi et al. 2007).
When considering only the cases that have at least one accept-
able solution generated by ZDOCK, the success rates of
pyDockTET for predicting an acceptable conformation in
the top 10 and 50 solutions are 69% and 77%, respectively,
whereas the success rates of pyDock alone are 62% and 69%,
respectively (Cheng et al. 2008).
Except in five known difficult cases (1BGX, 1I4D, 1SBB,
1HE8, 1IB1), several acceptable solutions have been found in
almost all docking cases with RMSDL ≤10 Å or RMSDL ≤4
Å within 10,000 default predictions yielded by FRODOCK
(Garzon et al. 2009). For 64% of acetylcholinesterase com-
plexes, the shape complementarity identified by HEX over-
laps with the native binding site (Wass et al. 2011). Further,
Cell-Dock was tested on the unbound structures of protein–
protein docking benchmark version 2.0 formed by 84 cases. In
89% of the cases using CELL-256 and in 85% of the cases
when using CELL-128, the docking poses are nearer to native
conformations. These results were also assessed by pyDOCK
based on electrostatics, desolvation, and van der Waals energy.
The scoring by pyDOCK showed a slightly better success rate
with CELL-256 than with CELL-128. With CELL-256,
19.7% of the cases obtained near native conformations within
the top 10 scoring solutions, whereas 18.3% of the cases
showed near native conformations within the top 10 scoring
solutions using CELL-128 (Pons et al. 2012). In both the
cases, the differences were minimal and the values in general
were similar to those achieved by pyDOCK when scoring
FTDOCK models (Pons et al. 2010).
According to the latest CAPRI experiments carried out in
2013, the ClusPro server was best in automated protein
docking equivalent to the best human predictor group.
HADDOCK (de Vries et al. 2010), SwarmDock (Torchala
et al. 2013), and PIE-Dock (Ravikant and Elber 2010) were
the next best. In the human predictor category, HADDOCK
(Dominguez et al. 2003) was given the first rank, followed by
SwarmDock (Venkatraman and Ritchie 2012). ICM
Biophys Rev
(Fernández-Recio et al. 2002) was ranked in the 2nd to 5th
positions (Kozakov et al. 2013; Lensink and Wodak 2013).
The predicted binding mode for the CCDC-Astex set of 85
diverse protein–ligand complexes is correct in approximately
80% of cases with rDock (Ruiz-Carmona et al. 2014). By
incorporating the electrostatic term, MEGADOCK 2.1 suc-
cessfully predicted at least one near-native decoy for 128 pro-
tein complexes in the bound set and 23 complexes in the
unbound set in the top 100 scored decoys. When compared
with ZDOCK 3.0, MEGADOCK 2.1 was less successful
(Ohue et al. 2014b).
Flexible docking
In standard virtual docking studies, ligands are freely docked
into a rigid receptor. However, it has become increasingly
clear that side chain flexibility plays a crucial role in ligand–
protein complexes. These changes allow the receptor to alter
its binding site according to the orientation of the ligand. The
ligand orients in a (6 + N)-dimensional space of translational,
rotational, and conformational variables in the anisotropic en-
vironment of the receptor (Jackson et al. 1998; Moon and
Howe 1991; Rotstein and Murcko 1993a, b; Nishibata and
Itai 1993). Four different strategies are currently in use for
docking flexible ligands, namely: (a) Monte Carlo or
molecular-dynamics docking of complete molecules; (b) in-
site combinatorial search, (c) ligand buildup; and (d) site map-
ping and fragment assembly.
Monte Carlo methods accept or reject the random changes
of the thermodynamic accessible states by using Metropolis
criteria (Metropolis and Ulam 1949). The configurations with
increase in temperature T will be accepted by slow cooling
through so-called simulated annealing (Kirkpatrick et al.
1983). The changes in conformations are quite large, allowing
the ligand to cross the energy barriers on the potential energy
surface. This technique of conformational searches combined
with the potentials of molecular affinity gives an efficient
method of substrate docking with known structures
(Goodsell and Olson 1990). Along with affinity potentials,
distance constraints were added as soft potentials in simulated
annealing (Yue 1990).
Examples of applying the Monte Carlo methods include an
earlier version of AutoDock (Novotny et al. 1989), ICM
(International Computer Management) (O’Sullivan et al.
1991), QXP (quick explore) (Pellegrini and Doniach 1993),
and Affinity (Ring et al. 1993). AutoDock 2.4 generates con-
formers in real space using Monte Carlo simulated annealing
with a rapid energy evaluation using molecular affinity grids
using common force fields (Leach 1994). ICM software gen-
erates the ligand in 3D grid space by Monte Carlo movements
and minimization of interaction potentials. Using this soft-
ware, the interactions between FNR (ferredoxin:NADP+
reductase) and its redox partners were modeled and their bind-
ing interfaces were predicted. The results obtained were high-
ly similar to FNR:Fd complexes of Anabaena and maize,
showing a good correlation computationally. QXP is a multi-
step docking program using a local Monte Carlo search with a
restricted rotational angle (Pellegrini and Doniach 1993).
Recently, a newly designed and implemented version of the
AutoDock program called AutoDock Vina has been released.
This version abandoned the former empirical scoring function
and GA-based optimizer, but adopted a new knowledge-based
scoring function with a Monte Carlo sampling technique and
the Broyden–Fletcher–Goldfarb–Shanno (BFGS) method for
local optimization. Their simulation results showed a signifi-
cant improvement in both prediction accuracy and docking
time. PSOVina is the first PSO (particle swarm optimization)
protein–ligand docking algorithm in the framework of
AutoDock Vina (Ng et al. 2015). Through careful integration
of Vina’s efficient local optimizer into the canonical PSO pro-
cedure and proper tuning of parameters, PSOVina achieved a
remarkable execution time reduction of 51–60% without
compromising the docking accuracies. In recent years, swarm
intelligence algorithms have emerged as a fast and reasonably
accurate technique in solving complex search problems in
computer science. To date, there exists only a handful of
swarm-based docking methods: SODOCK, a hybrid of PSO
and Solis and Wets’ local search method (Chen et al. 2007);
PLANTS, an ant colony optimization method (Korb et al.
2009); pso@autodock, a velocity adaptive and regenerative
constricted PSO method (Namasivayam and Günther 2007);
ParaDockS, a parallel docking suite having PSO as the opti-
mization algorithm (Banitt and Wolfson 2011); and
FIPSDock, the fully informed PSO method (Liu et al. 2013).
Three of the programs were modifications of the popular
open-source docking program AutoDock, albeit different ver-
sions, and all of them showed better predictive performance
when compared to the original AutoDock implementation.
Furthermore, a novel search method called QPSO-ls
(quantum-behaved particle swarm optimization) was intro-
duced for solving a highly flexible docking problem, which
is a hybrid of quantum-behaved particle swarm optimization
(QPSO) and a local search method of Solis and Wets (Fu et al.
2015). In another program called GalaxyDock, the receptor
side chains were preselected and globally optimized using an
AutoDock-based algorithm for flexible side-chain docking
(Shin and Seok 2012). FLIPDock uses the AutoDock force
field for generating multiple receptor conformations, termed
as the flexibility tree (FT) (Zhao and Sanner 2007).
Furthermore, ‘RosettaLigand’ uses a low-resolution docking
in the initial step combined with translational and rotational
adjustments (DeLuca et al. 2015). GOLD explores the flexi-
bility of the ligand through the process of evolution by using a
genetic algorithm and displaces loosely bound water on ligand
binding (Jones et al. 1995, 1997). Later, a wide range of

nuclear magnetic resonance (NMR) and available experimen-
tal as well as bioinformatics data was used to drive the
docking process in HADDOCK (Dominguez et al. 2003).
Previous modeling studies on protein–DNA and protein–
RNA complexes using NMR data have been shown to be
successful (Gu et al. 2015; Bursulaya et al. 2003; Paul and
Rognan 2002; Berman et al. 2002). The various degrees of
conformational flexibility of DNA were sampled by the semi-
flexibility of sugar-phosphate backbone and DNA base pairs
for further docking calculations. In FTDOCK, the docking
score is measured by rotating and translating the protein along
the DNA using shape and electrostatic complementarity by
approximate flexibility (Bruccoleri and Karplus 1990).
Further rotamer libraries can be used to reduce the side chain
placement problem to a combinatorial optimization problem
with the minimum energy, i.e., the global minimum energy
conformation (GMEC) (Kohlbacher and Lenhof 2000;
Canutescu et al. 2003). One of these methods is based on
the dead-end elimination (DEE) theorem of Desmet et al.
(1992). Later, GMEC was investigated as the convex hull of
all feasible solutions with some classes of facet-defining in-
equalities in a branch-and-cut algorithm. The side chain con-
formations generated by these techniques are then subjected to
a geometry optimization with a molecular mechanics force
field. Finally, the binding free energy of the optimized struc-
ture is estimated (Jackson and Sternberg 1995).
Further, the algorithms were developed to build ligands
directly in the binding site in flexible-docking and design
strategy. One of these was the de novo design of peptide in-
hibitors using a library of low-energy conformations of isolat-
ed amino acid residues as building blocks (Moon and Howe
1991). Subsequently, this method was extended to a non-
peptide ligand design using functional groups or single atoms
using GroupBuild and LEGEND (Nishibata and Itai 1993;
Rotstein and Murcko 1993a, b). Goodford introduced the idea
of using functional groups (water, methyl group, amine nitro-
gen, carboxy oxygen, and hydroxyl) as molecular probes to
map the binding site of a macromolecule (Goodford 1985).
Thus, the energy contour surfaces for the various probes dif-
ferentiate regions of attraction between the probe and protein.
The procedure is well suited to multiple-copy techniques
(Miranker and Karplus 1991). The goal of fragment-
assembly approaches, pioneered by Lewis and Dean (1989a,
b), is to connect the individual molecular fragments into a
single viable molecule. The CLIX program attempts to make
a pair of favorable interactions in the binding site of the pro-
tein with a pair of chemical substitutions (Lawrence and Davis
1992). LUDI places molecular fragments to form hydrogen
bonds with the enzyme so that the hydrophobic pockets are
filled. These fragments are then linked together with suitable
spacers (Böhm 1992). The linked-fragment approach of
Verlinde and coworkers are based on shape descriptors
(Verlinde et al. 1992). Caflisch and coworkers used MCSS
Biophys Rev
(maximal common substructure search) against HIV protease
to map a binding site and constructed peptide inhibitors by
building bonds to connect the various minima they found
(Caflisch et al. 1993). In HOOK, MCSS is also used in the
mapping stage, but the minima are connected by a database of
molecular scaffolds for possible connectors (Eisen et al.
1994). FlexX uses a tree-search technique for placing the li-
gand into the active site, incrementally starting with the base
fragment (Rarey et al. 1996).
Unlike other docking programs, Glide performs a complete
systematic search of the conformational, orientational, and
positional space of the docked ligand with the OPLS-AA
force field (Optimized Potentials for Liquid Simulations).
The best possible conformation is further refined using
Monte Carlo sampling (Friesner et al. 2004). SLIDE
(‘Screening for Ligands by Induced-fit Docking,
Efficiently’) optimization is based on the mean-field theory,
balancing flexibility between the ligand and the protein side
chains (Schnecke et al. 1998). Further, a surface-based
molecular similarity method was implemented in Surflex
(Jain 2003) to rapidly generate suitable putative poses for
molecular fragments using the Hammerhead docking sys-
tem (Jain 2003). In addition, a multi-objective docking
strategy, MoDock, has been proposed to further improve
the pose prediction with the available scoring functions
divided into the following three types: force field-based,
empirical-based, and knowledge-based. The results obtained
indicate that the multi-objective strategy can enhance the pose
prediction power of docking with the available scoring
functions (Gu et al. 2015).
Accuracy of flexible docking
Initially, three different docking programs (Dock, FlexX, and
GOLD), with six different scoring functions (Chemscore,
Dock, FlexX, Fresno, Gold, Pmf score) were evaluated
against thymidine kinase (TK) and estrogen receptor to mea-
sure the accuracy of virtual screening methods. Out of the
three docking programs, GOLD showed 60% docking accu-
racy with less than 1.2 Å RMSD, including the worst docked
orientation, with an RMSD of 3.1 Å. Surprisingly, both Dock
as well as FlexX were not able to produce a reasonable solu-
tion for at least three TK ligands (IdU (5-iododeoxyuridine),
hmtt (6-[6-hydroxymethy-5-methyl-2,4-dioxo-hexahydro-
pyrimidin-5-yl-methyl]-5-methyl-1H-pyrimidin-2,4-dione),
and mct ((North)-methanocarba-thymidine) for Dock; hmtt,
ganciclovir, and penciclovir for FlexX). Furthermore, the
best docking poses for ERα receptor with raloxifene, 4-
hydroxytamoxifen, were obtained using GOLD and, to
some extent, with FlexX. On the other hand, DOCK failed
completely to predict a reliable pose for raloxifene.
However, no relationship was found between the docking
Biophys Rev
accuracy and ranking score with these programs (Bissantz
et al. 2000).
In 2003, five docking programs, DOCK 4.0, FlexX 1.8,
AutoDock 3.0, GOLD 1.2, and ICM 2.8, were accessed with
a dataset of 37 protein–ligand complexes and screening the
compounds containing 10,037 entries against 11 different pro-
teins. The results revealed that ICM provided the highest
docking accuracy against these receptors, with a value of
0.93 compared to AutoDock, DOCK, FlexX, and GOLD,
with acceptable accuracies of 0.47, 0.31, 0.35, and 0.52, re-
spectively. In 17 cases, ICM predicted the original ligands
within the top 1% of the total library screened with 50% of
the potentially active compounds falling under ∼1.5% of top
scoring solutions, while DOCK and FlexX predicted only
∼9% of potentially active compounds. It was also found that
∼46%, 30%, 35%, 46%, and 76% of the molecules were
docked correctly within 2 Å RMSD by AutoDock, DOCK,
FlexX, GOLD, and ICM, respectively (Bursulaya et al. 2003).
Furthermore, in 2004, eight docking programs were evalu-
ated with 100 protein–ligand complexes (Paul and Rognan
2002) from the Protein Data Bank (PDB) (Berman et al.
2002). At an RMSD cutoff of 2 Å, 50–55% of the ligands
were successfully docked using FlexX, Glide, GOLD, and
Surflex, whereas the success rates of DOCK, FRED, SLIDE,
and QXP did not exceed 40%. Using the protein-bound X-ray
conformation, OMEGA was able to predict at least one con-
formation closer than 2 Å for 99% of 100 ligands. With ran-
dom ligand conformations, the docking poses obtained with
FRED were satisfactory, with RMSDs between 1.76 and 2.14
Å of docked poses from X-ray conformation. All these
docking programs performed well with small hydrophobic
ligands, while the performance of GOLD and Surflex
remained roughly unchanged. Moreover, Glide and FRED
are still efficient in ligand placement with a poor ranking abil-
ity (Kellenberger et al. 2004).
In the same year of 2004, three highly regarded docking
programs, namely, Glide, GOLD, and ICM, were evaluated
on a vertex dataset of 150 diverse protein–ligand complexes to
predict their ability to reproduce crystallographic binding ori-
entations. In 61% of the cases, Glide correctly identified the
crystallographic pose within 2.0 Å, compared to GOLD with
48% and 45% for ICM (Perola et al. 2004). In regards to
ligand complexity, all these docking programs performed
well, with the ligands having ten or fewer rotatable bonds.
However, LigandFit identified 75% of its close conformations
when the ligands have ten or fewer rotatable bonds, while
FlexX identified 69% for less than ten rotatable bonds, which
increases to 92% if the ligand has 15 or fewer degrees of
freedom. In contrast, the sensitivity of Glide is less, with a
78% success rate with smaller complexity less than 15, while
GOLD is the least sensitive of all (Kontoyianni et al. 2004).
Evaluation of known crystal structures of 40 zinc-
dependent metalloproteinase ligand complexes showed the
lowest energy conformations by GOLD and DrugScore with
a proper ZBG (zinc binding group) binding. However,
DOCK, GOLD, and DrugScore produced RMSD values
greater than 8 and improper ZBG binding, showing significant
differences between the docked pose and crystal structures. In
contrast, AutoDock and FlexX gave better results, with
RMSDs of 2.91 and 2.63 Å and a proper ZBG binding. If
the RMSD limit is increased to 2.5 Å, the percentage of the
well-docked poses with good/fair ZBG binding increased to
90% for all five approaches (Hu et al. 2004). At the 2% level
of predicting top-scoring molecules, Glide identifies known
active molecules for four of the five protein targets. However,
for the 10 and 20% levels, Glide was the only program which
identified one or more of the known active molecules for
each of the five target proteins. The same 2% level of
success was achieved when 5% of the top-scoring mole-
cules were considered by DOCKVISION and Glide. All
the other programs achieved between 10 and 20% level of
success by identifying one or more active seeds for four
of the five targets (Cummings et al. 2005).
Further results against 164 targets show that ICM and Glide
produce the lowest average RMSDs of 1.08 and 2.37 Å
matching with the native ligands, while GOLD and FlexX
fared worse, with RMSDs of 2.80 and 3.98 Å, respectively.
At the RMSD cutoff of 2.0 Å, ICM and Glide showed success
rates of 91 and 63%, respectively, by classifying 149 out of
164 and 104 out of 164 compounds correctly within this
threshold. GOLD also performed reasonably well by classify-
ing 91 from 164 (55%), while FlexX performed less well with
70 from 164, a percentage of 42%. ICM and Glide again
performed well at the more stringent RMSD cutoff of 1.0 Å,
correctly docking 93 out of 164 and 81 out of 164, leading to
success rates of 57 and 49%, respectively. GOLD was suc-
cessful in 64 out of 164 cases, for a success rate of 39%, and
FlexX was successful with a rate of 26% (42 out of 164)
(Chen et al. 2006). With eight protein targets, 50% of the
ligands were placed well for five targets by at least one pro-
gram. Indeed, 90% of the ligands could be docked with the
correct orientation and 100% could be docked in the correct
location for several protein targets (Warren et al. 2006). The
RMSD-based evaluations against 116 complexes of 13 types
revealed that no docking program was significantly superior
to GOLD. Thirteen complexes found solutions with an RMSD
of 2 Å or better only by GOLD, and no solution was
found by either AutoDock or DOCK alone. The sizes of
the binding sites for the complexes that were successfully
solved only by GOLD were widely distributed, from 2253
to 7900 Å, and represented the various protein types
(Onodera et al. 2007).
Later, ten docking programs and 37 scoring functions were
analyzed against seven protein types to predict the binding
mode, lead identification using virtual screening, and lead
optimization. Out of these ten programs, Glide, GOLD, and

QXP showed success for 61–63% of the cases with an RMSD
cutoff of 1 Å. At this cutoff, the docking was successful in
only 48% and 54% of the cases with FLEXX and Surflex,
respectively. With an RMSD threshold of 2 Å, 80–90% of
the ligands using Glide, GOLD, Surflex, and QXP, while
66% and 62% of the cases in FLEXX and FRED, respectively,
were place within 2.0 Å of the X-ray pose. Lastly, DOCK and
SLIDE placed only 50% of the ligands within the 2 Å RMSD
threshold. Studies also showed that GOLD performed well
with hydrophilic targets where there is some lipophilic char-
acter in the active site (i.e., thermolysins and PPAR-γ).
Contrary to GOLD, both LigandFit and Glide performed well
with COX-2, a target with a mainly hydrophobic binding
pocket (Kontoyianni et al. 2004).
Furthermore, seven commonly used programs were evalu-
ated on the PDBbind database with 1300 protein complexes
(Plewczynski et al. 2011). The results showed that Surflex,
FlexX, LigandFit, eHiTS, and GOLD were reasonable, with
failed complexes amounting to not more than 30, while 60%
of their complexes in GOLD and eHiTS have their top score
conformations below 2 Å. AutoDock failed to dock nearly 90
pairs, while only 1170 (90% of the entire database) complexes
overcame the Glide ligand restraints on the number of rotat-
able bonds to 35 and ligand size of 200 atoms. Both pose
prediction and scoring capabilities of Glide, AutoDock, and
Surflex achieved results of around 50%. The docking accura-
cy by LigandFit reached nearly 60% with a higher number of
rotatable bonds, whereas medium and weak ones achieved
only 50%. The level of correlation for hydrophobic molecules
is 0.2, though the ligand–protein contacts were based on van
der Waals and polar interactions.
Later, 19 docking protocols were used to predict bound
conformations for the 136 compounds of seven different tar-
gets (kinase, protease, isomerase, polymerase, synthetase,
metalloprotease, and NHR) of the available protein/ligand
crystal structures. For all targets except HCVP, at least one
program was able to dock 40% of the ligands within 2 Å of
the crystal conformation. In 2010, four popular docking pro-
grams were evaluated, Glide (version 4.5), GOLD (version
3.2), LigandFit (version 2.3), and Surflex (version 2.0), on a
test set of 195 protein–ligand complexes. Out of these four
docking programs, GOLD and Surflex processed well with
the dataset, while Glide and LigandFit failed to process 25
and 8 complexes, respectively. Except for Surflex, the docking
solutions produced in 40% of the cases by other programs
were less than 1.0 Å of the RMSD, whereas Glide and
GOLD showed a 60% success rate on this highly diverse test.
Based on these results, these docking programs were ranked
as Glide > GOLD + gold score > GOLD + Chemscore ∼
GOLD + ASP ∼ Ligandfit > Surflex (Li et al. 2010).
Recently, ten docking programs were evaluated. The suc-
cess rate for the top scored and best poses varied from 40% to
60% and 60% to 80%, respectively. The RMSD obtained is
Biophys Rev
less than 2 Å between the top scored pose and the native pose.
On the basis of the results for the top scored poses, the perfor-
mance of the academic programs conform to the following
order: LeDock (57.4%) > rDock (50.3%) ∼ AutoDock Vina
(49.0%) > AutoDock (PSO) (47.3%) > UCSF DOCK (44.0%)
> AutoDock (LGA) (37.4%), and that of the commercial pro-
grams confirm to the following order: GOLD (59.8%) > Glide
(XP) (57.8%) > Glide (SP) (53.8%) > Surflex-Dock (53.2%) >
LigandFit (46.1%) > MOE-Dock (45.6%). The averaged suc-
cess rates of the commercial docking programs in predicting
the top scored poses and best poses are 54.0% and 67.8%,
which can be compared to academic programs, with success
rates of 47.4% and 68.4%, respectively (Wang et al. 2016).
This shows that all these docking algorithms were able to
explore the conformational space to generate correctly docked
poses in the binding pockets sufficiently well on a diverse set
of protein–ligand complexes.
In general. Glide performs well with diversified binding
sites and flexibility of the ligand, while ICM and GOLD per-
form significantly poorer when binding sites are mainly influ-
enced by hydrophobic contacts. These results also show that
the difference between the commercial and academic pro-
grams was not obvious, even though the capability of
predicting the ligand binding poses by the commercial pro-
grams is slightly better than that of the academic programs
from a global perspective.
Conclusions
Structure-based drug design is a powerful technique for the
rapid identification of small molecules against the 3D struc-
ture of the macromolecular targets available by either X-ray,
NMR, or homology models. Because of abundant information
regarding the sequences and structures of the proteins, the
structural information of individual proteins and their in-
teractions became very important for further drug therapy.
Although many docking programs exist for conformational
searching and binding pose prediction, the scoring func-
tions are not accurate and need to be improved further.
Nevertheless, despite the drawbacks of each docking strategy,
active research is taking place to address all the issues regarding
scoring, explicit protein flexibility, explicit water, etc.
Even in the absence of knowledge regarding the binding
site and limited backbone movements, a variety of search
algorithms have been developed for protein–protein docking
over the past two decades. As rigid body docking can system-
atically explore the shape complementarity between proteins,
this may not work well for docking the proteins that are crys-
tallized separately. Thus, a high-resolution protocol is very
much needed to understand the basic principles to detect the
underlying mechanism of protein–protein interactions and ac-
tual binding with other proteins. Rescoring using empirical
Biophys Rev
potentials may not even eliminate all the false-positives.
Even fine tuning of individual protein–protein interactions
by redesigning the protein interface depends on the accu-
rate structure of the protein complex generated by high-
resolution docking protocols.
Although, ZDOCK, rDOCK, and HEX provided the
results with high docking accuracy, the provided com-
plexes are not highly useful to design the inhibitors for
the protein interfaces due to constraints in rigid body
docking. Due to this, flexible approaches were developed
that generally examine very limited conformations com-
pared to the rigid body methods. These docking methods
predict binding poses most likely to occur on the broad
surface regions and then define the sites into high-affinity
complex structures. The best example is the HADDOCK
software, which has been quite successful in resolving a
large number of accurate models for protein–protein com-
plexes. One good example is the study of the complex
formed between plectasin, a member of the innate immune
system, and the bacterial wall precursor lipid II. The study
has clearly identified the residues involved at the binding
site between the two proteins, providing valuable informa-
tion for the design of novel antibiotics.
However, the absolute energies associated with the inter-
molecular interaction are not estimated with satisfactory accu-
racy by the current algorithms. The major issues of solvent
effects, entropic effects, and receptor flexibility still need
to be handled with special attention. As of now, some
methods like MOE-Dock, GOLD, Glide, FlexX, Surflex,
etc. that deal with side chain flexibility have been proven
effective and adequate in most of the cases. The realistic
interactions between small molecules and receptors still
rely on experimental technology. Moreover, using the cur-
rent docking methods, although they discriminate between
different ligands based on binding affinity with high accu-
racy, the mode of binding, solvent effects, entropic effects,
and effects of protonation states of the charged residues in
the active site are still major problems. With the aid of
community efforts such as CAPRI (Critical Assessment of
PRediction of Interactions), a large number of docking
algorithms and their limitations were overcome with
benchmark testing. But the problem of flexibility is still
under investigation and with the accelerated pace of research
in this area, it will be tackled soon in the near future.
Compliance with ethical standards
Conflict of interest Nataraj S. Pagadala declares that he has no conflict
of interest. Khajamohiddin Syed declares that he has no conflict of inter-
est. Jack Tuszynski declares that he has no conflict of interest.
Ethical approval This article does not contain any studies with human
participants or animals performed by any of the authors.
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